[gentoo-commits] repo/gentoo:master commit in: dev-perl/Bio-DB-HTS/, dev-perl/Bio-DB-HTS/files/

[Marek Szuba]

commit:     0243d563e8de7d1eb26227665892172dbf3379f6
Author:     Marek Szuba <marecki <AT> gentoo <DOT> org>
AuthorDate: Tue May  1 13:48:24 2018 +0000
Commit:     Marek Szuba <marecki <AT> gentoo <DOT> org>
CommitDate: Tue May  1 15:13:53 2018 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=0243d563

dev-perl/Bio-DB-HTS: remove old

Package-Manager: Portage-2.3.24, Repoman-2.3.6

 dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.10.ebuild         | 32 ---------------
 dev-perl/Bio-DB-HTS/Manifest                       |  1 -
 .../files/2.10-build_search_for_so.patch           | 29 -------------
 .../files/2.10-build_split_htslib_opts.patch       | 48 ----------------------
 4 files changed, 110 deletions(-)

diff --git a/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.10.ebuild b/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.10.ebuild
deleted file mode 100644
index 0a150300213..00000000000
--- a/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.10.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DIST_AUTHOR=AVULLO
-DIST_VERSION=2.10
-
-inherit perl-module
-
-DESCRIPTION="Perl bindings for sci-libs/htslib"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-
-RDEPEND="sci-biology/bioperl
-	sci-libs/htslib:="
-DEPEND="${RDEPEND}
-	dev-perl/Module-Build
-	test? ( dev-perl/Test-LeakTrace )"
-
-PATCHES=(
-	"${FILESDIR}/2.10-build_search_for_so.patch"
-	"${FILESDIR}/2.10-build_split_htslib_opts.patch"
-)
-
-src_configure() {
-	local myconf="--htslib-includedir=${EPREFIX}/usr/include/htslib --htslib-libdir=${EPREFIX}/usr/$(get_libdir)"
-	perl-module_src_configure
-}

diff --git a/dev-perl/Bio-DB-HTS/Manifest b/dev-perl/Bio-DB-HTS/Manifest
index 6770bf66986..3eaf22e7a99 100644
--- a/dev-perl/Bio-DB-HTS/Manifest
+++ b/dev-perl/Bio-DB-HTS/Manifest
@@ -1,2 +1 @@
-DIST Bio-DB-HTS-2.10.tar.gz 5245650 BLAKE2B a52d9b1e19d5920d61dd365eacfd1a40726500e25a3ab516df5a1d59a7a9d79ce02db7a2145801b6af5df2c41c95e80b49a39db83d27fd7ff3cf88ba0e6a328d SHA512 4e7c01022d9edf48a0e0dcffcbccf34812f236d1b581760ac115c323de5779fb6212eb4ad7d1953811930a6137cc8f5f59028c73d645d1ca5fb6118dd846ad57
 DIST Bio-DB-HTS-2.11.tar.gz 5250814 BLAKE2B d77ccacebf339a33ab106b997139cdbf79f6c28269a832305e660b28370aca82b4c9824773acdbf8f59b18dd61f40346a9870578dba7b5b989b0f3bc9ad14b35 SHA512 114d90fe92b684250183b45b4d23d2dd45ecdcb2fa54f7b1c311ed668d8e87953adb861f709a0a48ff2b873ce777b21bc3b557bafa0df216b9a71b59facff6fd

diff --git a/dev-perl/Bio-DB-HTS/files/2.10-build_search_for_so.patch b/dev-perl/Bio-DB-HTS/files/2.10-build_search_for_so.patch
deleted file mode 100644
index b3d11bbbe7a..00000000000
--- a/dev-perl/Bio-DB-HTS/files/2.10-build_search_for_so.patch
+++ /dev/null
@@ -1,29 +0,0 @@
---- a/Build.PL
-+++ b/Build.PL
-@@ -125,7 +125,7 @@
- 
-     my $hts_lib     = "$root";
-     my $hts_include = "$root/htslib";
--    if (-f "$hts_lib/libhts.a" && -f "$hts_include/hts.h") {
-+    if ((-f "$hts_lib/libhts.so" || -f "$hts_lib/libhts.a") && -f "$hts_include/hts.h") {
-         $self->config_data('hts_lib'     => $hts_lib);
-         $self->config_data('hts_include' => $hts_include);
-         return 1;
-@@ -145,7 +145,7 @@
- 
-     my $hts_lib     = "$root/lib";
-     my $hts_include = "$root/include/htslib";
--    if (-f "$hts_lib/libhts.a" && -f "$hts_include/hts.h") {
-+    if ((-f "$hts_lib/libhts.so" || -f "$hts_lib/libhts.a") && -f "$hts_include/hts.h") {
-         $self->config_data('hts_lib'     => $hts_lib);
-         $self->config_data('hts_include' => $hts_include);
-         return 1;
-@@ -164,7 +164,7 @@
- This module requires htslib (http://htslib/org)
- Install it if you have not done so already.
- 
--This script will attempt to locate htslib by looking for hts.h and libhts.a in:
-+This script will attempt to locate htslib by looking for hts.h and libhts.so/libhts.a in:
- 
-   1. --htslib command line argument
-   2. HTSLIB_DIR environment variable

diff --git a/dev-perl/Bio-DB-HTS/files/2.10-build_split_htslib_opts.patch b/dev-perl/Bio-DB-HTS/files/2.10-build_split_htslib_opts.patch
deleted file mode 100644
index d68bc54e40d..00000000000
--- a/dev-perl/Bio-DB-HTS/files/2.10-build_split_htslib_opts.patch
+++ /dev/null
@@ -1,48 +0,0 @@
---- a/Build.PL
-+++ b/Build.PL
-@@ -68,7 +68,13 @@
-     # If either of these are set, we expect to find the htslib files there:
-     # (They're explicitly set by the user, so we shouldn't fall back to
-     # finding another copy somewhere else.)
--    if (my $dir = $self->args('htslib')) {
-+    if (my ($incdir, $libdir) = ($self->args('htslib-includedir'), $self->args('htslib-libdir'))) {
-+        return 1 if $self->find_hts_in_split_install_dirs($incdir, $libdir);
-+        $self->die_hts_not_found(
-+            "--htslib-includedir '$incdir' or --htslib-libdir '$libdir' command line parameters do not contain expected files\n"
-+        );
-+    }
-+    elsif (my $dir = $self->args('htslib')) {
-         return 1 if $self->find_hts_in_build_dir($dir);
-         return 1 if $self->find_hts_in_install_dir($dir);
-         $self->die_hts_not_found(
-@@ -155,6 +161,22 @@
-     }
- }
- 
-+sub find_hts_in_split_install_dirs {
-+    my ($self, $hts_include, $hts_lib) = @_;
-+
-+    chomp($hts_include);
-+    chomp($hts_lib);
-+
-+    if ((-f "$hts_lib/libhts.so" || -f "$hts_lib/libhts.a") && -f "$hts_include/hts.h") {
-+        $self->config_data('hts_lib'     => $hts_lib);
-+        $self->config_data('hts_include' => $hts_include);
-+        return 1;
-+    }
-+    else {
-+        return 0;
-+    }
-+}
-+
- sub die_hts_not_found {
-     my ($self, $msg) = @_;
- 
-@@ -166,6 +188,7 @@
- 
- This script will attempt to locate htslib by looking for hts.h and libhts.so/libhts.a in:
- 
-+  0. --htslib-includedir and --htslib-libdir command line arguments
-   1. --htslib command line argument
-   2. HTSLIB_DIR environment variable
-   3. --prefix command line argument (which also sets installation location)